Although Ganon was defeated, his legacy lives on. His followers continue to terrorise Hyrule, and believe their master may be resurrected if they manage to kill Link. Meanwhile, on his 16th birthday, the unsuspecting Link learns that he is part of a much grander scheme. Long ago, the first Zelda was cast into a deep sleep from which she would only awaken if all three pieces of the Triforce are reunited. The third piece, the Triforce of Courage, is Link's destiny.

He must break the six seals protecting the missing Triforce, by battling through six new dungeons in a previously unexplored area of Hyrule. Again, combat is based on sword- and shieldplay, this time with much more emphasis on action as Link can block and parry both high and low attacks. This is a result of the new viewpoint - dungeons are now side-on multilevel scrollers. The overworld remains top-down but empty of true combat: encountering a monster in the field transports him to a side-on battle arena. Fighting results in gaining experience which can be used to level up Link's stats, but the acquisition of new equipment and skills (including a collection of magic spells) remains the core of the adventure.

You are trapped in a small square grid in the centre of the screen, and a collection of coloured shapes advance toward you from all sides. If they reach the square, the game is over. To destroy them, you can "zoop;" shooting out from the square and destroying any shapes of your own colour. Zooping a shape of a different colour will swap theirs and yours, so careful planning can allow you to whittle down the enemy ranks. Each level, as well as speeding up the action, features increasingly clashing, multicoloured backgrounds designed to confuse.